Variant report

Variant	rs9728400
Chromosome Location	chr1:153595056-153595057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153541191..153544684-chr1:153594586..153597033,3	MCF-7	breast:
2	chr1:153539227..153541131-chr1:153594881..153597093,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10158761	0.85[EUR][1000 genomes]
rs61805740	0.85[EUR][1000 genomes]
rs6688800	1.00[ASN][1000 genomes]
rs73009954	1.00[ASN][1000 genomes]
rs7549308	0.85[EUR][1000 genomes]
rs9660389	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660416	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728059	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153585600-153596400	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:153585600-153597600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
5	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
6	chr1:153586000-153595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:153586000-153596200	Weak transcription	Fetal Kidney	kidney
8	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
9	chr1:153588600-153598800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:153589000-153596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:153589200-153595200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:153589200-153599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:153589400-153595400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:153589400-153596400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:153589400-153598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:153589600-153597800	Weak transcription	HepG2	liver
17	chr1:153590000-153598600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:153590200-153596200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:153590400-153596200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:153590400-153596200	Strong transcription	Osteobl	bone
21	chr1:153590400-153596400	Weak transcription	Liver	Liver
22	chr1:153590400-153596400	Weak transcription	Right Ventricle	heart
23	chr1:153590400-153596400	Weak transcription	Spleen	Spleen
24	chr1:153590400-153597800	Weak transcription	Right Atrium	heart
25	chr1:153590400-153598200	Weak transcription	Colonic Mucosa	Colon
26	chr1:153590400-153598200	Weak transcription	Pancreas	Pancrea
27	chr1:153590400-153598600	Weak transcription	Brain Anterior Caudate	brain
28	chr1:153590400-153598600	Weak transcription	Esophagus	oesophagus
29	chr1:153590400-153598600	Weak transcription	Gastric	stomach
30	chr1:153590400-153598600	Weak transcription	K562	blood
31	chr1:153590600-153595200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:153590600-153595200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:153590600-153595200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:153590600-153595400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:153590600-153596200	Weak transcription	Brain Substantia Nigra	brain
36	chr1:153590600-153596200	Strong transcription	Fetal Stomach	stomach
37	chr1:153590600-153596400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:153590600-153596400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr1:153590600-153596600	Weak transcription	Fetal Heart	heart
40	chr1:153590600-153598000	Weak transcription	Small Intestine	intestine
41	chr1:153590600-153598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:153590600-153599400	Weak transcription	Primary B cells from cord blood	blood
43	chr1:153590800-153595400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:153590800-153596200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:153590800-153598800	Weak transcription	Stomach Mucosa	stomach
46	chr1:153591000-153595400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:153591000-153595600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:153591000-153595800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:153591000-153596200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:153591000-153596400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links